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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.26

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-04-01, 12:35 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data

        nf-core/quantms Software Versions

        nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms

        Process Name Software Version
        ASSEMBLE_EMPIRICAL_LIBRARY DIA-NN 1.8.1
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        DIANNCFG sdrf-pipelines 0.0.21
        DIANNCONVERT sdrf-pipelines 0.0.21
        DIANNSUMMARY DIA-NN 1.8.1
        DIANN_PRELIMINARY_ANALYSIS DIA-NN 1.8.1
        INDIVIDUAL_FINAL_ANALYSIS DIA-NN 1.8.1
        MSSTATS bioconductor-msstats 4.2.0
        r-base 4.1.2
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        THERMORAWFILEPARSER ThermoRawFileParser 1.3.4
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/quantms

        Core Nextflow options

        runName
        voluminous_thompson
        containerEngine
        docker
        launchDir
        /home/chengxin/newPR/quantms
        workDir
        /home/chengxin/newPR/quantms/work
        projectDir
        /home/chengxin/newPR/quantms
        userName
        chengxin
        profile
        test_dia,docker
        configFiles
        /home/chengxin/newPR/quantms/nextflow.config

        Input/output options

        input
        /home/chengxin/diatestdata/PXD026600/PXD026600Partial2.sdrf.tsv
        outdir
        ./results_dia

        Protein database

        database
        /home/chengxin/diatestdata/PXD026600/REF_EColi_K12_UPS1_combined.fasta

        Database search

        allowed_missed_cleavages
        1
        instrument
        N/A
        max_precursor_charge
        3
        min_peptide_length
        15
        max_peptide_length
        30
        max_mods
        2

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8
        min_pr_mz
        350
        max_pr_mz
        950
        min_fr_mz
        500
        max_fr_mz
        1500
        diann_normalize
        N/A

        Statistical post-processing

        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Institutional config options

        config_profile_name
        Test profile for DIA
        config_profile_description
        Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        2d

        Generic options

        hostnames
        N/A

        MultiQC v1.26 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.